Cryptic marine barriers to gene flow in a vulnerable coastal species, the dugong (Dugong dugon)

Despite the lack of obvious physical barriers and their ability to travel significant distances, many marine mammals exhibit substantial population structuring over relatively short geographical distances. The dugong (Dugong dugon), the only extant representative of family Dugongidae, is listed as Vulnerable to Extinction globally. We investigated the genetic population structure of dugongs in the shallow coastal waters along >2,000 km of the eastern Queensland coast, including the Great Barrier Reef region. Microsatellite genotypes for 22 loci in 293 dugongs, SNP genotypes based on 10,690 loci in 43 dugongs, and 410 bp mitochondrial control-region sequences from 639 dugongs were analyzed. Clustering analysis techniques consistently identified an abrupt genetic break in the Whitsunday Islands region (20.3 degrees S), which interrupts an overall pattern of isolation-by-distance. Geographic distance was relatively more important than sea-surface temperature and seagrass distribution in explaining pairwise microsatellite genetic distances. The cause of reduced dispersal across this region is unknown but might relate to an unusual tidal and current mix, termed the "sticky-water" effect, and/or a break in the geographical distribution of off-shore seagrass meadows. The genetic structure suggests distinct breeding units north and south of the Whitsunday Islands region for consideration in further developing management plans for Queensland dugongs.